Simultaneous Bayesian inference of phylogeny and molecular coevolution
Simultaneous Bayesian inference of phylogeny and molecular coevolution
复制标题
DOI：
10.1073/pnas.1813836116
复制
发表时间：
2019-03-12
影响因子：
11.1
通讯作者：
Salamin, Nicolas
中科院分区：
文献类型：
--
作者：
Meyer, Xavier;Dib, Linda;Salamin, Nicolas
分子共同进化的模式可以揭示有机分子内部或之间的结构和功能限制。当考虑潜在的进化过程时，这些模式被更好地理解，这使我们能够将位点依赖进化(共同进化)的信号从基因共同祖先的影响中分离出来。相反，在研究基因历史时忽视位点的依赖进化会对推断的系统发育树的准确性产生负面影响。尽管分子共同进化和系统发育历史是相互依存的，但对这两个过程的分析是分开进行的，这一选择取决于计算的便利性，但代价是准确性。我们提出了一种贝叶斯方法和相关软件来推断一个比对的多少个和哪些位点按照独立的或成对依赖的进化过程进化，并同时估计序列之间的系统发育关系。我们在合成数据集上验证了我们的方法，并通过将16S rRNA分子与其已知分子结构进行比较来挑战我们关于16S rRNA分子共同进化的预测。最后，我们使用合成数据集、真核生物的16S rRNA分子和10个额外的蛋白质编码基因序列来评估在位点之间独立的假设下推断的系统发育树的准确性。我们的结果表明，推断系统发育树，同时解释依赖的位置进化，显着影响系统发育和进化过程的估计。
Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.